CFAP100 p.Ala179=
c.537G>A · VCV3390018
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00921%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -8.6 | GERP -3.9 |
| Overall | ||
| CADD | 0.139 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00921%
East Asian · 4/43,408 alleles
Filtering AF
0.00305%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00185%
Overall
0.000632%
10/1,583,118 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00921% | 10,852 |
| South Asian | 0.00229% | 43,715 |
| Remaining individualsnot grpmax-eligible | 0.00163% | 61,268 |
| African / African-American | 0.00136% | 73,554 |
| European (non-Finnish) | 0.000171% | 583,250 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CFAP100
- Protein
- p.Ala179=
- Coding
- c.537G>A
- MANE Select
- NM_182628
- Type
- single nucleotide variant
- Location
- chr3:126418661 (GRCh38)
- Gene constraint
- LOEUF 1.041 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.85 · 1 PDB
- Residue 179
- the 'microtubule-binding' region
Similar variants
- CFAP100 p.Ala179Val Uncertain significance ★ ⚠ same residue
- CFAP100 p.Ala126Ser Uncertain significance ★ ⚠ same type
- CFAP100 p.Ala224Asp Uncertain significance ★ ⚠ same type
- CFAP100 p.Ala499Thr Uncertain significance ★ ⚠ same type
- CFAP100 p.Ala563Val Uncertain significance ★ ⚠ same type
- CFAP100 p.Ala565Val Uncertain significance ★ ⚠ same type
- CFAP100 p.Ala73Pro Uncertain significance ★ ⚠ same type
- CFAP100 p.Arg103Gln Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cfap100-p-ala179 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown